Comparison of threshold selection methods for microarray gene co-expression matrices

<p>Abstract</p> <p>Background</p> <p>Network and clustering analyses of microarray co-expression correlation data often require application of a threshold to discard small correlations, thus reducing computational demands and decreasing the number of uninformative correlations. This study investigated threshold selection in the context of combinatorial network analysis of transcriptome data.</p> <p>Findings</p> <p>Six conceptually diverse methods - based on number of maximal cliques, correlation of control spots with expressed genes, top 1% of correlations, spectral graph clustering, Bonferroni correction of p-values, and statistical power - were used to estimate a correlation threshold for three time-series microarray datasets. The validity of thresholds was tested by comparison to thresholds derived from Gene Ontology information. Stability and reliability of the best methods were evaluated with block bootstrapping.</p> <p>Two threshold methods, number of maximal cliques and spectral graph, used information in the correlation matrix structure and performed well in terms of stability. Comparison to Gene Ontology found thresholds from number of maximal cliques extracted from a co-expression matrix were the most biologically valid. Approaches to improve both methods were suggested.</p> <p>Conclusion</p> <p>Threshold selection approaches based on network structure of gene relationships gave thresholds with greater relevance to curated biological relationships than approaches based on statistical pair-wise relationships.</p

Predisposition to Cancer Caused by Genetic and Functional Defects of Mammalian Atad5

ATAD5, the human ortholog of yeast Elg1, plays a role in PCNA deubiquitination. Since PCNA modification is important to regulate DNA damage bypass, ATAD5 may be important for suppression of genomic instability in mammals in vivo. To test this hypothesis, we generated heterozygous (Atad5+/m) mice that were haploinsuffficient for Atad5. Atad5+/m mice displayed high levels of genomic instability in vivo, and Atad5+/m mouse embryonic fibroblasts (MEFs) exhibited molecular defects in PCNA deubiquitination in response to DNA damage, as well as DNA damage hypersensitivity and high levels of genomic instability, apoptosis, and aneuploidy. Importantly, 90% of haploinsufficient Atad5+/m mice developed tumors, including sarcomas, carcinomas, and adenocarcinomas, between 11 and 20 months of age. High levels of genomic alterations were evident in tumors that arose in the Atad5+/m mice. Consistent with a role for Atad5 in suppressing tumorigenesis, we also identified somatic mutations of ATAD5 in 4.6% of sporadic human endometrial tumors, including two nonsense mutations that resulted in loss of proper ATAD5 function. Taken together, our findings indicate that loss-of-function mutations in mammalian Atad5 are sufficient to cause genomic instability and tumorigenesis

Humoral and intestinal immunity induced by new schedules of bivalent oral poliovirus vaccine and one or two doses of inactivated poliovirus vaccine in Latin American infants: an open-label randomised controlled trial

© 2016 Elsevier Ltd Background Replacement of the trivalent oral poliovirus vaccine (tOPV) with bivalent types 1 and 3 oral poliovirus vaccine (bOPV) and global introduction of inactivated poliovirus vaccine (IPV) are major steps in the polio endgame strategy. In this study, we assessed humoral and intestinal immunity in Latin American infants after three doses of bOPV combined with zero, one, or two doses of IPV. Methods This open-label randomised controlled multicentre trial was part of a larger study. 6-week-old full-term infants due for their first polio vaccinations, who were healthy on physical examination, with no obvious medical conditions and no known chronic medical disorders, were enrolled from four investigational sites in Colombia, Dominican Republic, Guatemala, and Panama. The infants were randomly assigned by permuted block randomisation (through the use of a computer-generated list, block size 36) to nine groups, of which five will be discussed in this report. These fi

Inactivated poliovirus vaccine given alone or in a sequential schedule with bivalent oral poliovirus vaccine in Chilean infants: a randomised, controlled, open-label, phase 4, non-inferiority study

Artículo de publicación ISIBackground Bivalent oral poliovirus vaccine (bOPV; types 1 and 3) is expected to replace trivalent OPV (tOPV) globally by April, 2016, preceded by the introduction of at least one dose of inactivated poliovirus vaccine (IPV) in routine immunisation programmes to eliminate vaccine-associated or vaccine-derived poliomyelitis from serotype 2 poliovirus. Because data are needed on sequential IPV bOPV schedules, we assessed the immunogenicity of two different IPV bOPV schedules compared with an all-IPV schedule in infants. Methods We did a randomised, controlled, open-label, non-inferiority trial with healthy, full-term (>2.5 kg birthweight) infants aged 8 weeks (+/- 7 days) at six well-child clinics in Santiago, Chile. We used supplied lists to randomly assign infants (1:1:1) to receive three polio vaccinations (IPV by injection or bOPV as oral drops) at age 8,16, and 24 weeks in one of three sequential schedules: IPV bOPV bOPV, IPV IPV bOPV, or IPV IPV IPV. We did the randomisation with blocks of 12 stratified by study site. All analyses were done in a masked manner. Co-primary outcomes were non-inferiority of the bOPV-containing schedules compared with the all-IPV schedule for seroconversion (within a 10% margin) and antibody titres (within two-thirds log(2) titres) to poliovirus serotypes land 3 at age 28 weeks, analysed in the per-protocol population. Secondary outcomes were seroconversion and titres to serotype 2 and faecal shedding for 4 weeks after a monovalent OPV type 2 challenge at age 28 weeks. Safety analyses were done in the intention-to-treat population. This trial is registered with ClinicalTrials.gov, number NCT01841671, and is dosed to new participants. Findings Between April 25 and August 1,2013, we assigned 570 infants to treatment: 190 to IPV bOPV bOPV, 192 to IPV IPV bOPV, and 188 to IPV IPV IPV. 564 (99%) were vaccinated and included in the intention-to-treat cohort, and 537 (94%) in the per-protocol analyses. In the IPV bOPV bOPV, IPV IPV bOPV, and IPV IPV IPV groups, respectively, the proportions of children with seroconversion to type 1 poliovirus were 166 (98.8%) of 168,95% CI 95-8-99.7; 178 (100%), 97.9-100-0; and 175 (100%), 97.9-100.0. Proportions with seroconvsion to type 3 poliovirus were 163 (98.2%) of 166,94.8-99.4; 177(100%), 97.9-100-0, and 172(98.9%) of 174,95.9-99.7. Non-inferiority was thus shown for the bOPV-containing schedules compared with the all-IPV schedule, with no significant differences between groups. In the IPV bOPV bOPV, IPV IPV bOPV, and IPV IPV IPV groups, respectively, the proportions of children with seroprotective antibody titres to type 1 poliovirus were 168 (98-8%) of 170, 95% CI 95-8-99.7; 181 (100%), 97.9-100.0; and 177 (100%), 97.9-100.0. Proportions to type 3 poliovirus were 166 (98-2%) of 169, 94.9-99.4; 180 (100%), 97-9400.0; and 174 (98.9%) of 176,96.0-99.7. Non-inferiority comparisons could not be done for this outcome because median litres for the groups receiving OPV were greater than the assay's upper limit of detection (log2 titres >10.5). The proportions of children seroconverting to type 2 poliovirus in the IPV bOPV bOPV, IPV IPV bOPV, and IPV IPV IPV groups, respectively, were 130 (77.4%) of 168, 95% CI 70.5-83.0; 169 (96.0%) of 176,92.0-98.0; and 175 (100%), 97.8-100. IPV bOPV schedules resulted in almost a 0.3 log reduction of type 2 faecal shedding compared with the IPV-only schedule. No participants died during the trial; 81 serious adverse events were reported, of which one was thought to be possibly vaccine-related (intestinal intussusception). Interpretation Seroconversion rates against polioviruses types 1 and 3 were non-inferior in sequential schedules containing IPV and bOPV, compared with an all-IPV schedule, and proportions of infants with protective antibodies were high after all three schedules. One or two doses of bOPV after IPV boosted intestinal immunity for poliovirus type 2, suggesting possible cross protection. Additionally, there was evidence of humoral priming for type 2 from one dose of IPV. Our findings could give policy makers flexibility when choosing a vaccination schedule, especially when trying to eliminate vaccine-associated and vaccine-derived poliomyelitis

Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features.

The broadly neutralizing antibody (bnAb) VRC01 is being evaluated for its efficacy to prevent HIV-1 infection in the Antibody Mediated Prevention (AMP) trials. A secondary objective of AMP utilizes sieve analysis to investigate how VRC01 prevention efficacy (PE) varies with HIV-1 envelope (Env) amino acid (AA) sequence features. An exhaustive analysis that tests how PE depends on every AA feature with sufficient variation would have low statistical power. To design an adequately powered primary sieve analysis for AMP, we modeled VRC01 neutralization as a function of Env AA sequence features of 611 HIV-1 gp160 pseudoviruses from the CATNAP database, with objectives: (1) to develop models that best predict the neutralization readouts; and (2) to rank AA features by their predictive importance with classification and regression methods. The dataset was split in half, and machine learning algorithms were applied to each half, each analyzed separately using cross-validation and hold-out validation. We selected Super Learner, a nonparametric ensemble-based cross-validated learning method, for advancement to the primary sieve analysis. This method predicted the dichotomous resistance outcome of whether the IC50 neutralization titer of VRC01 for a given Env pseudovirus is right-censored (indicating resistance) with an average validated AUC of 0.868 across the two hold-out datasets. Quantitative log IC50 was predicted with an average validated R2 of 0.355. Features predicting neutralization sensitivity or resistance included 26 surface-accessible residues in the VRC01 and CD4 binding footprints, the length of gp120, the length of Env, the number of cysteines in gp120, the number of cysteines in Env, and 4 potential N-linked glycosylation sites; the top features will be advanced to the primary sieve analysis. This modeling framework may also inform the study of VRC01 in the treatment of HIV-infected persons

A first-in-human germline-targeting HIV nanoparticle vaccine induced broad and publicly targeted helper T cell responses

The engineered outer domain germline targeting version 8 (eOD-GT8) 60-mer nanoparticle was designed to prime VRC01-class HIV-specific B cells that would need to be matured, through additional heterologous immunizations, into B cells that are able to produce broadly neutralizing antibodies. CD4 T cell help will be critical for the development of such high-affinity neutralizing antibody responses. Thus, we assessed the induction and epitope specificities of the vaccine-specific T cells from the IAVI G001 phase 1 clinical trial that tested immunization with eOD-GT8 60-mer adjuvanted with AS01. Robust polyfunctional CD4 T cells specific for eOD-GT8 and the lumazine synthase (LumSyn) component of eOD-GT8 60-mer were induced after two vaccinations with either the 20- or 100-microgram dose. Antigen-specific CD4 T helper responses to eOD-GT8 and LumSyn were observed in 84 and 93% of vaccine recipients, respectively. CD4 helper T cell epitope hotspots preferentially targeted across participants were identified within both the eOD-GT8 and LumSyn proteins. CD4 T cell responses specific to one of these three LumSyn epitope hotspots were observed in 85% of vaccine recipients. Last, we found that induction of vaccine-specific peripheral CD4 T cells correlated with expansion of eOD-GT8-specific memory B cells. Our findings demonstrate strong human CD4 T cell responses to an HIV vaccine candidate priming immunogen and identify immunodominant CD4 T cell epitopes that might improve human immune responses either to heterologous boost immunogens after this prime vaccination or to other human vaccine immunogens

Immune correlates analysis of the PREVENT-19 COVID-19 vaccine efficacy clinical trial

Authors have previously reported on the efficacy and safety of the recombinant spike protein nanoparticle vaccine, NVX-CoV2373, in healthy adults. In this work, they assess anti-spike binding IgG, anti-RBD binding IgG and neutralising antibody titer as correlates of risk and protection against COVID-19